Actaually, WorldEdit is getting closer to being compatible with cubic chunks. The most recent builds should work above y=256, there is a test build that works below y=0, and there are plans to make all of WorldEdit work correctly with cubic chunks.

Currently this mos is alpha version. All by itself it has some known issues. Mod compatiblity could be better.

A lot of it is likely to change in future Minecraft versions. 1.13.2 should be a big step for world generation compatibility. While progress on mod compatibility is slow, more mods become compatible over time. Eventually there may be time when you can just put cubic chunks into an average modpack and it will work.

Right now if you want a modpack with cubic chunks, you really have to design around it, and avoid mods that cause issues.